The invention relates to a RNA interference sequence targeting a cucumber mosaic virus, an expression vector thereof and application. The cucumber mosaic virus targeted RNA interference sequence is double-stranded RNA, is composed of a sense strand and an antisense strand, and is an interference sequence GT1 of a GT1 gene specifically targeting CMV-1a protein, or an interference sequence GT2 of a GT2 gene specifically targeting CMV-1a protein, or an interference sequence GT3 of a GT3 gene specifically targeting CMV-2a protein, or an interference sequence GT4 of a GT4 gene specifically targeting CMV-2a protein, or an interference sequence GT5 of a GT5 gene specifically targeting CMV-CP protein, or an interference sequence GT16 of a GT6 gene specifically targeting CMV-MP protein. The double-stranded RNA interference sequence is used for degrading target messenger RNA, reducing expression of target protein, effectively silencing CMV genes and controlling CMV infection, and has the characteristic of environmental friendliness and high commercial application value.